In its native environment, the structure of DNA is strongly influenced by the presence of cellular components such as histones, which bind the DNA helping to stabilize it and assist with its organization during cell division. The familiar shape of chromosomes is due primarily to a complex condensation process caused by interactions between DNA and these nuclear proteins which bind to it.
Stripped of all of these other materials, DNA behaves quite differently. The conformation and motion of DNA by itself in solution are dominated by constant thermal bombardment and statistical effects. On the nanometer scale, DNA is a stiff molecule. The stiffness of the molecule is described by a parameter called the persistence length. Despite the relative stiffness of DNA, for sufficiently long molecules it tends to form a spherical “blob”, which is the technical term used by the polymer dynamics community to refer to the conformation of a polymer in free solution. The size of this blob depends on the length of the DNA molecule and the persistence length. DNA is a highly charged molecule, and because the normal aqueous buffer solutions used with DNA have high densities of free ions, the electrostatic forces on DNA molecules are strongly influenced by the screening effects of charges called counterions which are attracted to the DNA molecule. Because the DNA molecules are charged, they move under the influence of an electric field, but the details of this motion are complicated by hydrodynamic interactions between molecules and their counterions. It turns out that the mobility (the ratio of the drift velocity to the applied field) does not depend on the size of the molecule. This is the reason gels are used for separating DNA—the interactions between the DNA and the polymer chains in the gel are responsible for the mobility differences between different sized molecules. Gels fail, however, when the DNA chains get very long. The field-induced elongation of the molecule in the axial direction spoils the length dependence of the mobility and for long chains there is no separation.
It is possible to extend the operational range of gel electrophoresis by reducing the field, but the time required for a separation quickly grows to unreasonable durations. A host of strategies for avoiding this limit have been developed, but still the separation of long DNA strands by gel electrophoresis is a time-consuming process.
There is a need for a separation technique that does not exhibit adverse length dependence. There is a further need for a long molecule separation technique that can be done in a short time.